A lot of motorcycle reboring is done in bike shops by mechanics, not machinists, using a simple boring bar machine. Centring the bore before reboring is often pretty, ahem, basic. Often just basically a tapered fitting on the boring bar that fits into the mouth of the bore while the cylinder is clamped down on the table. The alignment does not have to be perfect. Within a thou or two would be plenty close enough. (There is plenty of side clearance on the gudgeon pin in one direction and almost infinite available variation fore and aft in the direction the crank rotates. Remember, the average engine is not "blueprinted" but relatively roughly put together under production tolerances.)
And, yes set up can be quite flimsy as cuts are small. Usually you are boring to 10 thou bigger than present, so five thou total depth of cut, or a bit less allowing for honing. So possibly done in one cut of four thou depth. Material is nice grade of cast iron so it machines beautifully.